more type fixes

Author: mr-c

cwltool/builder.py

@@ -31,13 +31,15 @@
 from .errors import WorkflowException
 from .loghandler import _logger
 from .mutation import MutationManager
-from .pathmapper import CONTENT_LIMIT, get_listing, normalizeFilesDirs
 from .stdfsaccess import StdFsAccess
 from .utils import (
+    CONTENT_LIMIT,
     CWLObjectType,
     CWLOutputType,
     aslist,
     docker_windows_path_adjust,
+    get_listing,
+    normalizeFilesDirs,
     onWindows,
     visit_class,
 )

cwltool/command_line_tool.py

@@ -46,14 +46,7 @@
 from .job import CommandLineJob, JobBase
 from .loghandler import _logger
 from .mutation import MutationManager
-from .pathmapper import (
-    PathMapper,
-    adjustDirObjs,
-    adjustFileObjs,
-    get_listing,
-    normalizeFilesDirs,
-    trim_listing,
-)
+from .pathmapper import PathMapper
 from .process import (
     Process,
     _logger_validation_warnings,
@@ -69,12 +62,17 @@
     CWLOutputType,
     JobsGeneratorType,
     OutputCallbackType,
+    adjustDirObjs,
+    adjustFileObjs,
     aslist,
     convert_pathsep_to_unix,
     docker_windows_path_adjust,
+    get_listing,
+    normalizeFilesDirs,
     onWindows,
     random_outdir,
     shared_file_lock,
+    trim_listing,
     upgrade_lock,
     visit_class,
     windows_default_container_id,
@@ -628,11 +626,15 @@ def update_status_output_callback(
                     initialWorkdir["listing"],
                 ):
                     if isinstance(t, Mapping) and "entry" in t:
-                        entry_exp = builder.do_eval(cast(str, t["entry"]), strip_whitespace=False)
+                        entry_exp = builder.do_eval(
+                            cast(str, t["entry"]), strip_whitespace=False
+                        )
                         for entry in aslist(entry_exp):
                             et = {"entry": entry}
                             if "entryname" in t:
-                                et["entryname"] = builder.do_eval(cast(str, t["entryname"]))
+                                et["entryname"] = builder.do_eval(
+                                    cast(str, t["entryname"])
+                                )
                             else:
                                 et["entryname"] = None
                             et["writable"] = t.get("writable", False)

cwltool/docker.py

@@ -22,11 +22,13 @@
 from .expression import JSON
 from .job import ContainerCommandLineJob
 from .loghandler import _logger
-from .pathmapper import MapperEnt, PathMapper, ensure_non_writable, ensure_writable
+from .pathmapper import MapperEnt, PathMapper
 from .utils import (
     DEFAULT_TMP_PREFIX,
     CWLObjectType,
     docker_windows_path_adjust,
+    ensure_non_writable,
+    ensure_writable,
     onWindows,
 )
 

cwltool/executors.py

@@ -427,3 +427,24 @@ def run_jobs(
             self.run_job(None, runtime_context)
 
         runtime_context.workflow_eval_lock.release()
+
+
+class NoopJobExecutor(JobExecutor):
+    """ Do nothing executor, for testing purposes only. """
+    def run_jobs(
+        self,
+        process: Process,
+        job_order_object: Dict[str, Any],
+        logger: logging.Logger,
+        runtime_context: RuntimeContext,
+    ) -> None:
+        pass
+
+    def execute(
+        self,
+        process: Process,
+        job_order_object: Dict[str, Any],
+        runtime_context: RuntimeContext,
+        logger: Optional[logging.Logger] = None,
+    )  -> Tuple[Union[Optional[CWLObjectType], MutableSequence[CWLObjectType]], str]:
+        return {}, "success"

cwltool/job.py

@@ -34,17 +34,18 @@
 
 import psutil
 import shellescape
-from prov.model import PROV
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dump, json_dumps
 from typing_extensions import TYPE_CHECKING
 
+from prov.model import PROV
+
 from .builder import Builder, HasReqsHints
 from .context import RuntimeContext, getdefault
 from .errors import UnsupportedRequirement, WorkflowException
 from .expression import JSON
 from .loghandler import _logger
-from .pathmapper import MapperEnt, PathMapper, ensure_non_writable, ensure_writable
+from .pathmapper import MapperEnt, PathMapper
 from .process import stage_files
 from .secrets import SecretStore
 from .utils import (
@@ -53,6 +54,8 @@
     Directory,
     bytes2str_in_dicts,
     copytree_with_merge,
+    ensure_non_writable,
+    ensure_writable,
     onWindows,
     processes_to_kill,
 )

cwltool/main.py

@@ -65,7 +65,6 @@
 from .loghandler import _logger, defaultStreamHandler
 from .mutation import MutationManager
 from .pack import pack
-from .pathmapper import adjustDirObjs, normalizeFilesDirs, trim_listing
 from .process import (
     CWL_IANA,
     Process,
@@ -88,8 +87,11 @@
 from .update import ALLUPDATES, UPDATES
 from .utils import (
     DEFAULT_TMP_PREFIX,
+    adjustDirObjs,
+    normalizeFilesDirs,
     onWindows,
     processes_to_kill,
+    trim_listing,
     versionstring,
     visit_class,
     windows_default_container_id,
@@ -640,11 +642,11 @@ class ProvLogFormatter(logging.Formatter):
     def __init__(self):  # type: () -> None
         super(ProvLogFormatter, self).__init__("[%(asctime)sZ] %(message)s")
 
-    def formatTime(self, record, datefmt=None):
-        # type: (logging.LogRecord, Optional[str]) -> str
-        record_time = time.gmtime(record.created)
-        formatted_time = time.strftime("%Y-%m-%dT%H:%M:%S", record_time)
-        with_msecs = "%s,%03d" % (formatted_time, record.msecs)
+    def formatTime(
+        self, record: logging.LogRecord, datefmt: Optional[str] = None
+    ) -> str:
+        formatted_time = time.strftime("%Y-%m-%dT%H:%M:%S", time.gmtime(record.created))
+        with_msecs = "%s,%03f" % (formatted_time, record.msecs)
         return with_msecs